RetrogeneDB ID: retro_lafr_194

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_1:99797001..99797334(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: MDK
• Ensembl ID: ENSLAFG00000015119
• Aliases: None
• Description: None

Sequence

>retro_lafr_194
ATGCAACACTGAGCCTTGCTCCTCCTCACCCTCCTTGCCCTACTGGTGCTCACTTCCTCAGTGGCCAAAAAGAAAGACAA
AGTGAAGAAGGACGGCCTGGGGAGCAAGTGCGCGGAGTGGACCTGGAGGCCCTGCACCCCCAGCAGCAAGAACTTCTCTG
TGGGCTTCCCTGAGGGCGTCTACAGGGCCCAGGCTCAGCGCGTCAGGTGTTAAGTGCCTTGCAACTGGAAGAAGGGTTTG
GAGCCTACTGCAAGTACAAGTTTGAGAGCTGGCATGTGTGTGATGGGGGCACAGGCACCCCAAAGAAGGCGTGGTATACT
GCCCAGTGCCAGG

Alignment

ORF - retro_lafr_194 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.91 %
• Parental protein coverage: 77.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MQHRAFLLFALLALLALTSAVAKNKDKVKKGGPGNECAEWTWGPCTPSSKDCGVGFREGTCGAQTQRIRC
          MQH.A.LL..LLALL.LTS.VAK.KDKVKK.G.G..CAEWTW.PCTPSSK...VGF.EG...AQ.QR.RC
Retrocopy MQH*ALLLLTLLALLVLTSSVAKKKDKVKKDGLGSKCAEWTWRPCTPSSKNFSVGFPEGVYRAQAQRVRC

Parental  RVPCNWKK-EFGADCKYKFESWGACDGGTGT-KARQGTLKKAR
          .VPCNWKK..FGA.CKYKFESW..CDGGTGT...R.G.L..AR
Retrocopy *VPCNWKK<GFGAYCKYKFESWHVCDGGTGT>QRRRGILPSAR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Loxodonta africana was not studied using RNA-Seq expression data.

ChIP-Seq

Loxodonta africana was not studied using ChIP-Seq data.

EST

Loxodonta africana was not studied using EST data.

TSS

Loxodonta africana was not studied using FANTOM5 data.

Lab

retro_lafr_194 was not experimentally validated.

Homology

Retrocopy orthology:

Loxodonta africana does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007740	1 retrocopy	retro_btau_655,
Echinops telfairi	ENSETEG00000016707	2 retrocopies	retro_etel_1929, retro_etel_947,
Loxodonta africana	ENSLAFG00000015119	1 retrocopy	retro_lafr_194 ,
Macaca mulatta	ENSMMUG00000021448	2 retrocopies	retro_mmul_1486, retro_mmul_466,